GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcm-large in Pedobacter sp. GW460-11-11-14-LB5

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate CA265_RS14780 CA265_RS14780 methylmalonyl-CoA mutase

Query= BRENDA::O74009
         (563 letters)



>FitnessBrowser__Pedo557:CA265_RS14780
          Length = 1129

 Score =  228 bits (580), Expect = 1e-63
 Identities = 142/370 (38%), Positives = 219/370 (59%), Gaps = 12/370 (3%)

Query: 195  LRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCA-ENVPKWNPISISGYHIREAGA 253
            +RGTVQ DILKE  A+ T IF  + ++R+  DI  Y   E V  +  +SISGYHI EAGA
Sbjct: 763  VRGTVQADILKEDQAQNTCIFSTEFALRMMGDIQKYFIDEKVRNFYSVSISGYHIAEAGA 822

Query: 254  NAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKF-RAARRLWA 312
            N + ++AFTL++G  +V+  + RGM +D FAP LSFFF+  N    E A   R ARR+WA
Sbjct: 823  NPISQLAFTLSNGFTFVEYYLSRGMHIDDFAPNLSFFFS--NGIDPEYAVIGRVARRIWA 880

Query: 313  YIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLHTNSY 372
              +K  +   N RS  L++H QT+G +L AQ+ + N +R  +QAL A+     SLHTN+Y
Sbjct: 881  KAIKNKYKG-NDRSQKLKYHIQTSGRSLHAQEIDFNDIRTTLQALYAIYDNCNSLHTNAY 939

Query: 373  DEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQ 432
            DEA++ PTE+SVR A+  Q II  E G+    +PL GA+ IE LTD + +  L   ++I 
Sbjct: 940  DEAITTPTEESVRRAMAIQLIINRELGLAKNENPLQGAFIIEELTDLVEDAVLAEFKRIN 999

Query: 433  KMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEP----IEVEILKVD 488
              GG++ A+E  Y + +I E +  Y+     G+  IVGVN F+        +  E+++  
Sbjct: 1000 DRGGVLGAMETMYQRGKIQEESLYYETLKHTGEYPIVGVNTFLNKNGSPTIVPGEVIRAT 1059

Query: 489  PSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEVTD 548
               ++ QI  L+K + +R+  +  + L +L+ +A   D N+   ++E  + + +L +++ 
Sbjct: 1060 EDEKQYQISALQKFQ-DRNADRAVDLLKQLQKSAIAGD-NIFEQLMEVCK-ICSLGQISK 1116

Query: 549  VLREIWGEYR 558
             L E+ G+YR
Sbjct: 1117 ALYEVGGQYR 1126



 Score = 75.5 bits (184), Expect = 1e-17
 Identities = 67/226 (29%), Positives = 108/226 (47%), Gaps = 16/226 (7%)

Query: 6   KEVLKKIKEEEKRW-EETTVKKFLEKAPERKEKFMTDDGFEIKRIYTPA--DLGEDWNYM 62
           K +L++  + ++ + EE  + K  +K  ++   + +     I ++  P   D G+   ++
Sbjct: 502 KRLLRQWPDTKRAYKEEFFIYKVRDKEIKQPLFYESLSKLNIPKVSLPRYEDWGDILRWL 561

Query: 63  EKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYL-LSQGQTGLSVAFD 121
                PGE+P+  GV+     G   T R +AG    E +NKR+ Y+ L Q    LS AFD
Sbjct: 562 LTENLPGEFPYAAGVFPLKREGEDPT-RMFAGEGGPERTNKRFHYVSLGQPAHRLSTAFD 620

Query: 122 LPTQLGYDSD-HPLAEGEVGKVGVAIDSLWDMRILFDGIPL--DKVSTSMTINSTAANLL 178
             T  G D    P   G++G  GV I +L D + L+ G  L     S SMTIN  A  LL
Sbjct: 621 SVTLYGEDPHIRPDIYGKIGNSGVCIATLDDAKKLYSGFDLCAPSTSVSMTINGPAPMLL 680

Query: 179 AMYILVAEEQGVSQEKLRGTVQNDILKEYIARGTYIFP----PQPS 220
             ++  A    + Q+  +  ++ND+ KE  A+   I+     P+PS
Sbjct: 681 GFFMNAA----IDQQCEKYIIENDLTKEVEAKIDAIYQAKNIPRPS 722


Lambda     K      H
   0.318    0.134    0.388 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1304
Number of extensions: 67
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 563
Length of database: 1129
Length adjustment: 41
Effective length of query: 522
Effective length of database: 1088
Effective search space:   567936
Effective search space used:   567936
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory